Single-cell expression profiling reveals dynamic flux of cardiac stromal, vascular and immune cells in health and injury

Besides cardiomyocytes (CM), the heart contains numerous interstitial cell types which play key roles in heart repair, regeneration and disease, including fibroblast, vascular and immune cells. However, a comprehensive understanding of this interactive cell community is lacking. We performed single-cell RNA-sequencing of the total non-CM fraction and enriched (Pdgfra-GFP⁺) fibroblast lineage cells from murine hearts at days 3 and 7 post-sham or myocardial infarction (MI) surgery. Clustering of >30,000 single cells identified >30 populations representing nine cell lineages, including a previously undescribed fibroblast lineage trajectory present in both sham and MI hearts leading to a uniquely activated cell state defined in part by a strong anti-WNT transcriptome signature. We also uncovered novel myofibroblast subtypes expressing either pro-fibrotic or anti-fibrotic signatures. Our data highlight non-linear dynamics in myeloid and fibroblast lineages after cardiac injury, and provide an entry point for deeper analysis of cardiac homeostasis, inflammation, fibrosis, repair and regeneration.

In our bodies, heart attacks lead to cell death and inflammation. This is then followed by a healing phase where the organ repairs itself. There are many types of heart cells, from muscle and pacemaker cells that help to create the beating motion, to so-called fibroblasts that act as a supporting network. Yet, it is still unclear how individual cells participate in the heart's response to injury.

All cells possess the same genetic information, but they turn on or off different genes depending on the specific tasks that they need to perform. Spotting which genes are activated in individual cells can therefore provide clues about their exact roles in the body. Until recently, technological limitations meant that this information was difficult to access, because it was only possible to capture the global response of a group of cells in a sample.

A new method called single-cell RNA sequencing is now allowing researchers to study the activities of many genes in thousands of individual cells at the same time. Here, Farbehi, Patrick et al. performed single-cell RNA sequencing on over 30,000 individual cells from healthy and injured mouse hearts. Computational approaches were then used to cluster cells into groups according to the activities of their genes.

The experiments identified over 30 distinct sub-types of cell, including several that were previously unknown. For example, a group of fibroblasts that express a gene called Wif1 was discovered. Previous genetic studies have shown that Wif1 is essential for the heart's response to injury. Further experiments by Farbehi, Patrick et al. indicated that this new sub-type of cells may control the timing of the different aspects of heart repair after damage.

Tens of millions of people around the world suffer from heart attacks and other heart diseases. Knowing how different types of heart cells participate in repair mechanisms may help to find new targets for drugs and other treatments.

Hif-1a suppresses ROS-induced proliferation of cardiac fibroblasts following myocardial infarction

We report that cardiac fibroblasts (CFs) and mesenchymal progenitors are more hypoxic than other cardiac interstitial populations, express more hypoxia-inducible factor 1α (HIF-1α), and exhibit increased glycolytic metabolism. CF-specific deletion of Hif-1a resulted in decreased HIF-1 target gene expression and increased mesenchymal progenitors in uninjured hearts and increased CF activation without proliferation following sham injury, as demonstrated using single-cell RNA sequencing (scRNA-seq). After myocardial infarction (MI), however, there was ∼50% increased CF proliferation and excessive scarring and contractile dysfunction, a scenario replicated in 3D engineered cardiac microtissues. CF proliferation was associated with higher reactive oxygen species (ROS) as occurred also in wild-type mice treated with the mitochondrial ROS generator MitoParaquat (MitoPQ). The mitochondrial-targeted antioxidant MitoTEMPO rescued Hif-1a mutant phenotypes. Thus, HIF-1α in CFs provides a critical braking mechanism against excessive post-ischemic CF activation and proliferation through regulation of mitochondrial ROS. CFs are potential cellular targets for designer antioxidant therapies in cardiovascular disease.

Sierra: discovery of differential transcript usage from polyA-captured single-cell RNA-seq data

High-throughput single-cell RNA-seq (scRNA-seq) is a powerful tool for studying gene expression in single cells. Most current scRNA-seq bioinformatics tools focus on analysing overall expression levels, largely ignoring alternative mRNA isoform expression. We present a computational pipeline, Sierra, that readily detects differential transcript usage from data generated by commonly used polyA-captured scRNA-seq technology. We validate Sierra by comparing cardiac scRNA-seq cell types to bulk RNA-seq of matched populations, finding significant overlap in differential transcripts. Sierra detects differential transcript usage across human peripheral blood mononuclear cells and the Tabula Muris, and 3 'UTR shortening in cardiac fibroblasts. Sierra is available at https://github.com/VCCRI/Sierra .

Single-cell transcriptomics for the assessment of cardiac disease

Cardiovascular disease is the leading cause of death globally. An advanced understanding of cardiovascular disease mechanisms is required to improve therapeutic strategies and patient risk stratification. State-of-the-art, large-scale, single-cell and single-nucleus transcriptomics facilitate the exploration of the cardiac cellular landscape at an unprecedented level, beyond its descriptive features, and can further our understanding of the mechanisms of disease and guide functional studies. In this Review, we provide an overview of the technical challenges in the experimental design of single-cell and single-nucleus transcriptomics studies, as well as a discussion of the type of inferences that can be made from the data derived from these studies. Furthermore, we describe novel findings derived from transcriptomics studies for each major cardiac cell type in both health and disease, and from development to adulthood. This Review also provides a guide to interpreting the exhaustive list of newly identified cardiac cell types and states, and highlights the consensus and discordances in annotation, indicating an urgent need for standardization. We describe advanced applications such as integration of single-cell data with spatial transcriptomics to map genes and cells on tissue and define cellular microenvironments that regulate homeostasis and disease progression. Finally, we discuss current and future translational and clinical implications of novel transcriptomics approaches, and provide an outlook of how these technologies will change the way we diagnose and treat heart disease.

Vascular cells improve functionality of human cardiac organoids

Crosstalk between cardiac cells is critical for heart performance. Here we show that vascular cells within human cardiac organoids (hCOs) enhance their maturation, force of contraction, and utility in disease modeling. Herein we optimize our protocol to generate vascular populations in addition to epicardial, fibroblast, and cardiomyocyte cells that self-organize into in-vivo-like structures in hCOs. We identify mechanisms of communication between endothelial cells, pericytes, fibroblasts, and cardiomyocytes that ultimately contribute to cardiac organoid maturation. In particular, (1) endothelial-derived LAMA5 regulates expression of mature sarcomeric proteins and contractility, and (2) paracrine platelet-derived growth factor receptor β (PDGFRβ) signaling from vascular cells upregulates matrix deposition to augment hCO contractile force. Finally, we demonstrate that vascular cells determine the magnitude of diastolic dysfunction caused by inflammatory factors and identify a paracrine role of endothelin driving dysfunction. Together this study highlights the importance and role of vascular cells in organoid models.

MyoD-family inhibitor proteins act as auxiliary subunits of Piezo channels

Piezo channels are critical cellular sensors of mechanical forces. Despite their large size, ubiquitous expression, and irreplaceable roles in an ever-growing list of physiological processes, few Piezo channel-binding proteins have emerged. In this work, we found that MyoD (myoblast determination)-family inhibitor proteins (MDFIC and MDFI) are PIEZO1/2 interacting partners. These transcriptional regulators bind to PIEZO1/2 channels, regulating channel inactivation. Using single-particle cryogenic electron microscopy, we mapped the interaction site in MDFIC to a lipidated, C-terminal helix that inserts laterally into the PIEZO1 pore module. These Piezo-interacting proteins fit all the criteria for auxiliary subunits, contribute to explaining the vastly different gating kinetics of endogenous Piezo channels observed in many cell types, and elucidate mechanisms potentially involved in human lymphatic vascular disease.

An image analysis protocol using CellProfiler for automated quantification of post-ischemic cardiac parameters

Quantitative assessment of post-ischemic cardiac remodeling is often hampered by tissue complexity and structural heterogeneity of the scar. Automated quantification of microscopy images offers an unbiased approach to reduce inter-observer variability. Here, we present a CellProfiler-based analytical pipeline for the high-throughput analysis of confocal images to quantify post-ischemic cardiac parameters. We describe image preprocessing and the quantification of capillary rarefaction, immune cell infiltration, cell death, and proliferating fibroblasts. This protocol can be adapted to other tissue types. For complete details on the use and execution of this profile, please refer to Janbandhu et al. (2021).

Quantitative trait and transcriptome analysis of genetic complexity underpinning cardiac interatrial septation in mice using an advanced intercross line

Unlike single-gene mutations leading to Mendelian conditions, common human diseases are likely to be emergent phenomena arising from multilayer, multiscale and highly interconnected interactions. Atrial and ventricular septal defects are the most common forms of cardiac congenital anomalies in humans. Atrial septal defects (ASD) show an open communication between left and right atria postnatally, potentially resulting in serious hemodynamic consequences if untreated. A milder form of atrial septal defect, patent foramen ovale (PFO), exists in about one quarter of the human population, strongly associated with ischaemic stroke and migraine. The anatomic liabilities and genetic and molecular basis of atrial septal defects remain unclear. Here, we advance our previous analysis of atrial septal variation through quantitative trait locus (QTL) mapping of an advanced intercross line (AIL) established between the inbred QSi5 and 129T2/SvEms mouse strains, that show extremes of septal phenotypes. Analysis resolved 37 unique septal QTL with high overlap between QTL for distinct septal traits and PFO as a binary trait. Whole genome sequencing of parental strains and filtering identified predicted functional variants, including in known human congenital heart disease genes. Transcriptome analysis of developing septa revealed downregulation of networks involving ribosome, nucleosome, mitochondrial and extracellular matrix biosynthesis in the 129T2/SvEms strain, potentially reflecting an essential role for growth and cellular maturation in septal development. Analysis of variant architecture across different gene features, including enhancers and promoters, provided evidence for involvement of non-coding as well as protein coding variants. Our study provides the first high resolution picture of genetic complexity and network liability underlying common congenital heart disease, with relevance to human ASD and PFO.

Abstract 12: Physiological Role of Endogenous Adult Cardiac Colony-forming Unit Fibroblasts

Colony-forming unit fibroblasts (CFU-Fs), analogous to those giving rise to bone marrow (BM) mesenchymal stem cells (MSCs), have been identified in different tissues. CFU-Fs are multipotent progenitor cells, with a supportive paracrine and immunomodulatory function. They share the expression of surface antigens, are capable of self-renewal, and to differentiate into osteogenic, adipogenic and chondrogenic lineages in vitro. Our laboratory has isolated, for the first time, CFU-Fs from the adult murine heart. These cells are included within the Sca1+ PDGFRα+ CD31- fraction of interstitial cells, mainly associated with microvessels and the perivascular adventitial niche of larger vessels. Here we show that resident cCFU-Fs, are quiescent in homeostatic conditions, relatively more hypoxic and have a lower metabolic profile compared to other interstitial cells. Treatment with PDGF-AB ligand stimulates cCFU-Fs to exit the quiescent state, potentially making them more responsive to mitogenic and differentiative factors. In a mouse with a H2B-eGFP fusion gene knocked-in the Pdgfrα locus, cCFU-Fs lay in the GFPhigh population. After myocardial infarction, a GFPmed population appears, which has partially lost the expression of Sca1 and PDGFRα proteins, and consists largely of activated myofibroblasts. Likely derived from cCFU-Fs or related stromal fraction, GFPmed cells are significantly reduced by inhibiting PDGFRα signalling and increased by systemic PDGF-AB treatment. Despite augmenting the GFPmed myofibroblasts-like population, short-term PDGF-AB treatment is beneficial, leading to reduced scar, and increased vascular density and ejection fraction. A crucial factor in cardiac repair is the fine balance between pro-inflammatory (type1) and pro-reparative/pro-angiogenic (type2) immune responses, which can be regulated by MSCs. interestingly PDGF-AB treatment seems to be associated with an earlier resolution of the type1 response at 5 days after MI, compared to controls. We hypothesize that the beneficial effects of short term PDGF-AB treatment are due to early activation of cCFU-Fs and stromal cells from quiescence, leading to enhanced pro-angiogenic, anti-apoptotic and immunomodulatory impacts.

Loss of conserved long non-coding RNA MIR503HG leads to altered NOTCH pathway signalling and left ventricular non-compaction cardiomyopathy

AIMS

The highly conserved long non-coding RNA (lncRNA) MIR505HG has been primarily recognized as a precursor for microRNAs (miR)-424 and miR-503. However, studies have since demonstrated that MIR503HG has distinct functions from its associated miRNAs, playing important roles in cell proliferation, invasion, apoptosis, and differentiation. While these miRNAs are known to influence cardiomyocyte differentiation, the specific role of MIR503HG in heart development remains unexplored. We seek to determine how MIR503HG deletion impacts ventricular chamber development and to identify underlying molecular mechanisms.

METHODS AND RESULTS

To study the role of the lncRNA in vivo, we generated a functional MIR503HG knockout mouse model (MIR503HG-/-) using a synthetic polyadenylation signal to terminate MIR503HG transcription without affecting miR-424/503 expression. We performed morphological analyses on embryonic and adult hearts using microCT along with cardiac functional analysis via transthoracic echocardiography. We further apply single-nuclei RNA sequencing (snRNA-seq) on adult hearts to identify potential molecular mechanisms underlying the observed phenotypes. Functional deletion of MIR503HG alone was associated with reduced compact myocardium thickness and increased trabecular myocardium in the left ventricle (LV) at embryonic day 17.5 compared to wild-type mice, indicating a LV non-compaction (LVNC) phenotype. Moreover, adult MIR503HG-/- mutant hearts showed increased trabecular complexity, impaired LV relaxation, and mitral valve regurgitation. SnRNA-seq further revealed altered expression of several genes associated with cardiomyocyte function and LVNC, including Actc1, Mib1, Mybpc3, and Myh7. Lastly, Notch1 activity was also significantly increased in mutant hearts which has been previously associated with LVNC.

CONCLUSION

MIR503HG plays a role in ventricular chamber development, and its deletion leads to an LVNC phenotype independent of the miRNA cluster within its locus, highlighting its importance in cardiac development and disease. We further suggest that abnormal Notch1 activity may underpin the LVNC phenotype presented.

Integration mapping of cardiac fibroblast single-cell transcriptomes elucidates cellular principles of fibrosis in diverse pathologies

Single-cell technology has allowed researchers to probe tissue complexity and dynamics at unprecedented depth in health and disease. However, the generation of high-dimensionality single-cell atlases and virtual three-dimensional tissues requires integrated reference maps that harmonize disparate experimental designs, analytical pipelines, and taxonomies. Here, we present a comprehensive single-cell transcriptome integration map of cardiac fibrosis, which underpins pathophysiology in most cardiovascular diseases. Our findings reveal similarity between cardiac fibroblast (CF) identities and dynamics in ischemic versus pressure overload models of cardiomyopathy. We also describe timelines for commitment of activated CFs to proliferation and myofibrogenesis, profibrotic and antifibrotic polarization of myofibroblasts and matrifibrocytes, and CF conservation across mouse and human healthy and diseased hearts. These insights have the potential to inform knowledge-based therapies.

FACS Enrichment of Total Interstitial Cells and Fibroblasts from Adult Mouse Ventricles

Besides cardiomyocytes, the heart contains numerous interstitial cell types, including cardiac fibroblasts, endothelial cells, immune (myeloid and lymphoid) cells, and mural cells (pericytes and vascular smooth muscle cells), which play key roles in heart repair, regeneration, and disease. We recently published a comprehensive map of cardiac stromal cell heterogeneity and flux in healthy and infarcted hearts using single-cell RNA sequencing (scRNA-seq) ( Farbehi et al., 2019 ). Here, we describe the FACS (Fluorescent Activated Cell Sorting)-based method used in that study for isolation of two cardiac cell fractions from adult mouse ventricles: the total interstitial cell population (TIP; non-cardiomyocytes) and enriched (Pdgfra-GFP⁺) cardiac fibroblasts.

Abstract B78: The X protein of hepatitis B virus induces PI3K/Akt pathway to overcome gentoxic stress-related cyclin D1 degradation and growth arrest

B78

Growth arrest represents an innate barrier to carcinogenesis. DNA damage and replicational stress are known to induce growth arrest and apoptotic death to avert genomic instability and consequently carcinogenesis. Working on the genotoxic stress induced by hydroxyurea and methylmethanesulfone, we observed a growth arrest at G1/S-phase that was mediated by destabilization of cyclin D1. The growth arrest was independent of the stability of cdc25A and preceded transcriptional up-regulation of p21waf1. Cyclin D1 destabilization involved its phosphorylation by GSK-3beta at threonine-286 since overexpression of the kinase-dead mutant of GSK-3beta or cyclin D1T286A mutant conferred stability to cyclin D1. Further, overexpression of cyclin D1T286A also helped in bypassing G1/S phase growth arrest. We also observed a rapid inactivation of Akt/PKB kinase in the presence of hydroxyurea. Enforced expression of the constitutively active Akt or viral oncoprotein HBx was sufficient to overcome growth arrest independent of ATR signaling and stabilized cyclin D1. Thus, the present work not only establishes cyclin D1 to be a novel mediator of genetoxic stress signaling but also explains how a deregulated mitogenic signaling or a viral oncoprotein can help bypass growth arrest.

Citation Information: Cancer Prev Res 2008;1(7 Suppl):B78.